Table 2.
Fourteen loci associated with small-molecule phenotypes with genome-wide significance in meta-analysis of five Finnish cohorts
| Newly identified loci | ||||||||||||
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| SNP | Chr. | Lead trait | Position | Coded allele | Other allele | P value | CAF | Effect size | s.e.m. | eQTL | Candidate gene | Genotyped |
| rs2160387 | 2 | Ala/Val | 65074414 | C | T | 2.62 × 10−22 | 0.41 | −0.17 | 0.02 | – | SLC1A4 | rs10211524 |
| rs1440581 | 4 | Fischer’s ratio | 89445446 | C | T | 1.96 × 10−16 | 0.47 | 0.13 | 0.02 | – | PPM1K | rs6841731 |
| rs2545801 | 5 | Phe | 176773945 | T | C | 8.70 × 10−11 | 0.73 | −0.12 | 0.02 | – | F12 | rs2731672 |
| rs2297644 | 10 | Gln/His | 99349729 | C | T | 1.23 × 10−12 | 0.20 | 0.15 | 0.02 | – | DHDPSL | rs11817730 |
| rs4788815 | 16 | Phe/Tyr | 70192312 | T | A | 1.54 × 10−17 | 0.64 | 0.15 | 0.02 | – | TAT | rs4788547 |
| 17-7083575 (rs117616209)a | 17 | Fischer’s ratio | 7083575 | T | C | 2.64 × 10−14 | 0.02 | −0.51 | 0.07 | – | SLC2A4 | –b |
| rs807669 | 22 | Citrate | 17534522 | C | T | 3.30 × 10−16 | 0.62 | −0.14 | 0.02 | CLTCL1 | SLC25A1 | rs712964 |
| Known loci | ||||||||||||
|
| ||||||||||||
| SNP | Chr. | Lead trait | Position | Coded allele | Other allele | P value | CAF | Effect size | s.e.m. | eQTL | Candidate gene, trait | |
|
| ||||||||||||
| rs1260326 | 2 | Ala/Gln | 27584444 | C | T | 2.59 × 10−18 | 0.65 | −0.15 | 0.02 | – | GCKR, TG31 | |
| rs560887 | 2 | Glc | 169471394 | G | A | 2.19 × 10−17 | 0.69 | 0.15 | 0.02 | – | G6PC2, Glc20 | |
| rs4241816 | 4 | His/Val | 187389321 | T | A | 5.58 × 10−13 | 0.57 | 0.12 | 0.02 | – | KLKB1, bradykinin8 | |
| rs6900341 | 6 | Ala/Tyr | 111901102 | G | T | 3.68 × 10−15 | 0.37 | 0.13 | 0.02 | – | SLC16A10, Ile, Tyr8 | |
| rs10830963 | 11 | Glc | 92348358 | G | C | 3.19 × 10−11 | 0.28 | 0.14 | 0.02 | – | MTNR1B, Glc21 | |
| rs2638315 | 12 | Gln/Glc | 55151323 | C | G | 2.43 × 10−35 | 0.17 | −0.29 | 0.02 | SPRYD4 | GLS2, Gln8 | |
Chr., chromosome; position, SNP position in NCBI human genome build 36; CAF, coded allele frequency; candidate gene, potential candidate gene in the region; candidate gene, trait, gene reported for the known locus and lead trait with which the gene was associated; genotyped, genome-wide significant SNP genotyped in at least three study cohorts in the region of association; Ala, alanine; Glc, glucose; Gln, glutamine; His, histidine; Ile, isoleucine; Phe, phenylalanine; TG, total triglyceride content; Tyr, tyrosine; Val, valine.
This locus would not have been identified using the HapMap 2 imputation reference panel.
Imputed SNPs that were validated by sequencing.